Second harmonic generation (SHG) microscopy is applied to image honey sugar crystals, with the advantage of avoiding the surrounding signal of the liquid honey. It is a non-contact method where the specialized preparation of the honey is not required. Since the crystallization process of honey depends upon its floral origin, among other conditions, analyzing its crystallographic behavior results in a challenging task as the crystals are mixed and overlapped. This work introduces a simple, multi-variable data analysis requiring only one SHG image, where its gray-level histogram was retrieved and processed from eight Mexican bee honey samples. These honey samples represent a broad range of regions from the central–east part of Mexico, describing different environments and climates. The results obtained with this simplified methodology can differentiate among the botanical origin of the honey samples at different crystallization times and storage conditions. A repeatability test was performed using three honey samples with different crystal morphologies to expand the method to all of the samples. The results show that the proposed methodology could be a helpful alternative to identifying the botanical origin of honey despite its crystallization time.